Graph construction method impacts variation representation and analyses in a bovine super-pangenome

This work focuses on comparing pangenome constructions methods for the downstream implications of how well (and truthfully) variation is converted into currently-useful formats like VCF.

This reposistory is currently a work-in-progress as code is centralised and cleaned up.

Components

This project involves multiple steps. We first

• construct pangenomes from 12 bovine assemblies with
  • minigraph
  • pggb
  • cactus
• decompose pangenomes into vcf
• compare vcf files for accuracy to assembly-called truth
• assess applications to new topics like VNTRs.

Citation

The preprint associated with this work can be found here.